Locus 1112

Sequence ID	2L_DroMel_CAF1
Location	3,011,164 – 3,011,389
Length	225
Max. P	0.993562

overview

Window 0

Location	3,011,164 – 3,011,273
Length	109
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	90.83
Mean single sequence MFE	-43.30
Consensus MFE	-36.77
Energy contribution	-36.66
Covariance contribution	-0.11
Combinations/Pair	1.06
Mean z-score	-2.71
Structure conservation index	0.85
SVM decision value	1.05
SVM RNA-class probability	0.907543
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3011164 109 + 22407834
AUUGGCAUUUCCGACUGGGAGACCGAGACUCGUCUUCAUUGAAAUCGAGCUCGGAGCUCAAAGCUUAGAGCCUCACAAUCGGACUGGGGACCC-----------GACUGGAUCCCAGUUU
.........(((((.((.(((.(((((.((((..(((...)))..))))))))).((((........))))))).)).)))))((((((.((.-----------....)).))))))... ( -42.50)
>DroSec_CAF1 18570 109 + 1
AUUGGCAUUUCCGACUGGGAGACCGAGACUCGUCUUCAUUGAAAUCGAGCUCGGAGCUCAAAGCUCAGAGCCCCACAAUCGGACUGGGGACCC-----------GACUGGAUCCCAGUUU
.........(((((.((((...(((((.((((..(((...)))..))))))))).((((........))))))))...)))))((((((.((.-----------....)).))))))... ( -42.60)
>DroEre_CAF1 19191 120 + 1
AUUGGCAUUUCCGACUGGGAGACCGAGACUCGUCUUCAUUGAAAUCGAGCUCGAAGCUCAGAGCUCAGAGCCUCACAAUCGGACUGGGCACCCAAACGGGGACUGACUGGAUCCCAGUUU
............((((((((..(((((.((((..(((...)))..)))))))).((.((((.((((((..((........)).)))))).(((....)))..)))))))..)))))))). ( -44.80)
>consensus
AUUGGCAUUUCCGACUGGGAGACCGAGACUCGUCUUCAUUGAAAUCGAGCUCGGAGCUCAAAGCUCAGAGCCUCACAAUCGGACUGGGGACCC___________GACUGGAUCCCAGUUU
.........(((((..((....))(((.((((..(((...)))..)))))))((.((((........)))).))....)))))((((((.((................)).))))))... (-36.77 = -36.66 +  -0.11)

alignment

secondary structure

dotplot

Window 1

Location	3,011,164 – 3,011,273
Length	109
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	90.83
Mean single sequence MFE	-48.33
Consensus MFE	-46.27
Energy contribution	-45.83
Covariance contribution	-0.44
Combinations/Pair	1.05
Mean z-score	-3.72
Structure conservation index	0.96
SVM decision value	2.41
SVM RNA-class probability	0.993562
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3011164 109 - 22407834
AAACUGGGAUCCAGUC-----------GGGUCCCCAGUCCGAUUGUGAGGCUCUAAGCUUUGAGCUCCGAGCUCGAUUUCAAUGAAGACGAGUCUCGGUCUCCCAGUCGGAAAUGCCAAU
...(((((((((....-----------)))).)))))((((((((.(((((((........)))).(((((((((.((((...)))).)))).))))).))).))))))))......... ( -48.50)
>DroSec_CAF1 18570 109 - 1
AAACUGGGAUCCAGUC-----------GGGUCCCCAGUCCGAUUGUGGGGCUCUGAGCUUUGAGCUCCGAGCUCGAUUUCAAUGAAGACGAGUCUCGGUCUCCCAGUCGGAAAUGCCAAU
...(((((((((....-----------)))).)))))((((((((.(((((...((((.....))))((((((((.((((...)))).)))).))))))))).))))))))......... ( -48.30)
>DroEre_CAF1 19191 120 - 1
AAACUGGGAUCCAGUCAGUCCCCGUUUGGGUGCCCAGUCCGAUUGUGAGGCUCUGAGCUCUGAGCUUCGAGCUCGAUUUCAAUGAAGACGAGUCUCGGUCUCCCAGUCGGAAAUGCCAAU
...(((((((((((...........)))))).)))))((((((((.(((((...((((.....))))((((((((.((((...)))).)))).))))))))).))))))))......... ( -48.20)
>consensus
AAACUGGGAUCCAGUC___________GGGUCCCCAGUCCGAUUGUGAGGCUCUGAGCUUUGAGCUCCGAGCUCGAUUUCAAUGAAGACGAGUCUCGGUCUCCCAGUCGGAAAUGCCAAU
...(((((((((...............)))).)))))((((((((.(((((((........)))).(((((((((.((((...)))).)))).))))).))).))))))))......... (-46.27 = -45.83 +  -0.44)

alignment

secondary structure

dotplot

Window 2

Location	3,011,244 – 3,011,349
Length	105
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	90.14
Mean single sequence MFE	-30.53
Consensus MFE	-26.39
Energy contribution	-26.72
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.45
Structure conservation index	0.86
SVM decision value	0.95
SVM RNA-class probability	0.889133
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3011244 105 + 22407834
GGACUGGGGACCC-----------GACUGGAUCCCAGUUUCAACUUGCACACGGCAUGGCAAUCAAAGCCAGUAAAUCUACACCAAAAGCAACAAUAGCCG----GGCUAACAACAACAA
(((((((((.((.-----------....)).)))))))))......((...((((.((((.......))))(((....)))................))))----.))............ ( -29.10)
>DroSec_CAF1 18650 105 + 1
GGACUGGGGACCC-----------GACUGGAUCCCAGUUUCAACUUGCACACGGCAUGGCAAUCACAGCCAGUAAAUCUACACCAAAAGCAACAAUAGCCG----GGCUAACAACAACAA
(((((((((.((.-----------....)).)))))))))......((...((((.((((.......))))(((....)))................))))----.))............ ( -29.10)
>DroEre_CAF1 19271 120 + 1
GGACUGGGCACCCAAACGGGGACUGACUGGAUCCCAGUUUCAACUUGCACACGGCAUGGCAAUCAAAGCCAGUAAAUCUACACCAAAAGCAACAAUAGCCGGGCGGGCUAACAACAACAA
((((((((...(((..((....).)..)))..))))))))...(((((...((((.((((.......))))(((....)))................)))).)))))............. ( -33.40)
>consensus
GGACUGGGGACCC___________GACUGGAUCCCAGUUUCAACUUGCACACGGCAUGGCAAUCAAAGCCAGUAAAUCUACACCAAAAGCAACAAUAGCCG____GGCUAACAACAACAA
(((((((((.((................)).)))))))))....((((....((..((((.......))))(((....))).))....))))...(((((.....))))).......... (-26.39 = -26.72 +   0.33)

alignment

secondary structure

dotplot

Window 3

Location	3,011,273 – 3,011,389
Length	116
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	97.19
Mean single sequence MFE	-23.40
Consensus MFE	-23.93
Energy contribution	-23.93
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.76
Structure conservation index	1.02
SVM decision value	0.91
SVM RNA-class probability	0.880822
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3011273 116 + 22407834
CAACUUGCACACGGCAUGGCAAUCAAAGCCAGUAAAUCUACACCAAAAGCAACAAUAGCCG----GGCUAACAACAACAACCAGAGCAAUAUUUGUGCUCAUUAAGCGUAACUGACACAC
......((...((((.((((.......))))(((....)))................))))----..................(((((.......))))).....))............. ( -22.20)
>DroSec_CAF1 18679 116 + 1
CAACUUGCACACGGCAUGGCAAUCACAGCCAGUAAAUCUACACCAAAAGCAACAAUAGCCG----GGCUAACAACAACAACCAGAGCAAUAUUUGUGCUCAUUAAGCGUAACUGACACAC
......((...((((.((((.......))))(((....)))................))))----..................(((((.......))))).....))............. ( -22.20)
>DroEre_CAF1 19311 120 + 1
CAACUUGCACACGGCAUGGCAAUCAAAGCCAGUAAAUCUACACCAAAAGCAACAAUAGCCGGGCGGGCUAACAACAACAACCAGAGCAAUAUUUGUGCUCAUUAAGCGUAACUGACACAC
...(((((...((((.((((.......))))(((....)))................)))).)))))................(((((.......))))).................... ( -25.80)
>consensus
CAACUUGCACACGGCAUGGCAAUCAAAGCCAGUAAAUCUACACCAAAAGCAACAAUAGCCG____GGCUAACAACAACAACCAGAGCAAUAUUUGUGCUCAUUAAGCGUAACUGACACAC
....((((....((..((((.......))))(((....))).))....((.....(((((.....))))).............(((((.......))))).....))))))......... (-23.93 = -23.93 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:54:01 2006